Stress-induced cell degeneration is often associated with protein misfolding and aggregation. As a protection mechanism against the cellular toxicity of misfolded proteins, protein aggregates trigger a universal heat shock response pathway which mediates expression of molecular chaperones. Insufficient protection may contribute to degenerative disorders such as Parkinson's and Alzheimer's disease, hallmarks which include susceptibility of certain cell types to degeneration and onset of aging. Here we report that heat shock of wild-type Drosophila induces loss of flight ability along with selective degeneration of neurons, glia and muscle cells comprising the flight motor. The susceptibility of these cell types is dependent upon age, being observed in older but not younger flies, and is suppressed by overexpression of molecular chaperones. These findings, together with further genetic analysis in Drosophila, may advance our understanding of cell type-selective and age-dependent degeneration in disease as well as potential therapeutic applications for molecular chaperones.